Research workbench
1.55 ångström crystal structure of N-acetylmuramic acid 6-phosphate etherase from yersinia enterocolitica.
Analyse 1.55 ångström crystal structure of N-acetylmuramic acid 6-phosphate etherase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4S12
- Type
- protein
- Length
- 870 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acetylmuramic acid 6-phosphate etherase
- EC
- 4.2.1.126
- UniProt
- E7B2C4
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 295 | 57% helix, 8% strand | E7B2C4 |
| B | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 287 | 54% helix, 10% strand | E7B2C4 |
| C | N-acetylmuramic acid 6-phosphate etherase (EC 4.2.1.126) | protein | 288 | 55% helix, 10% strand | E7B2C4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.77 | 0.79 | 87 | SO4 |
| 2 | 613 | 0.68 | 0.77 | 67 | SO4 |
| 3 | 179 | 0.50 | 0.77 | 25 | empty |
| 4 | 115 | 0.47 | 0.79 | 22 | SO4 |
| 5 | 120 | 0.38 | 0.74 | 24 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 2949 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 451 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4S12 · 1.55 Angstrom Crystal Structure of N-acetylmuramic acid 6-phosphate Etherase from… · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt E7B2C4
- Elsewhere: RCSB PDB 4S12 · PDBe 4S12 · UniProt E7B2C4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.